The present invention relates to a process for producing a target fermentation product. More particularly, the present invention relates to a process for over-producing a target fermentation product in a microorganism having a mutation which causes auxotrophic growth of the microorganism, but that does not compromise its ability to over-produce the target fermentation product. Host cells and polynucleotide sequences used in the process are also provided.
Many commercially valuable products are produced by fermentation reactions. For example, riboflavin, which is an essential vitamin that is required by all bacteria, animals, and plants, is synthesized by plants and bacteria, however, it cannot be produced by higher animals, which must acquire it from their diet.
Riboflavin is produced commercially for use as a food and feed additive by, for example, fermentation reactions using Ashbya govsypii, Eremothecium ashbyii, or Candida flareri cells. (See e.g., Ainsworth, G. C. and Sussman, A. S., The Fungi, Academic Press, New York (1965); Heefner, D. L., et al., WO 88/09822; Hickey, R. J., Production of Riboflavin by Fermentation, in Industrial Fermentation (Underkofler, L. A. and Hickey, R. J., eds.) pp. 157-190, Chemical Publishing Co., New York (1954); and Perlman, D., et al., Fermentation Ind. Eng. Chem. 44:1996-2001 (1952).
The enzymes required to catalyze the biosynthesis of riboflavin from guanosine triphosphate (GTP) and ribulose-5-phosphate are encoded by four genes (ribG, ribB, ribA, and ribH) in B. subtilis. See, FIG. 1A. These genes are located in an operon, the gene order of which differs from the order of the enzymatic reactions catalyzed by the enzymes. For example, GTP cyclohydrolase II, which catalyzes the first step in riboflavin biosynthesis is encoded by the third gene in the operon, ribA. See, FIG. 2. The ribA protein also encodes a second enzymatic activity, i.e., DHB synthase, which catalyzes the conversion of ribulose-5-phosphate to the four-carbon unit DHB. Deaminase and reductase are encoded by the first gene of the operon, ribG. The bi-functionality of the ribA and ribG gene products may facilitate a coordinated riboflavin precursor flux. The penultimate step in riboflavin biosynthesis is catalyzed by lumazine (Lum) synthase, the product of the last rib gene, ribH. Riboflavin synthase, which controls the last step of the pathway, is encoded by the second gene of the operon, ribB. The function of the gene X (FIG. 1) located at the 3xe2x80x2 end of the rib operon is, at present, unclear, however, its gene product is not required for riboflavin synthesis.
Transcription of the riboflavin operon from the ribP1 promoter is controlled by an attenuation mechanism involving a regulatory leader region located between ribP1 and ribG. RibO mutations within this leader region result in deregulated expression of the riboflavin operon. Deregulated expression is also observed in strains containing missense mutations in the ribC gene. The ribC gene has recently been shown to encode the flavin kinase/FAD synthase of B. subtilis. See, Mack, M., et al., J. Bact., 180:950-55 (1998). Deregulating mutations reduce the flavokinase activity of the ribC gene product resulting in reduced intracellular concentrations of flavinmononucleotide (FMN), the effector molecule of the riboflavin regulatory system.
Recently, a Bacillus subtilis microorganism was genetically engineered to produce high yields of riboflavin during a short fermentation cycle. See, Perkins, J. B., U.S. Pat. No. 5,837,528 (xe2x80x9cPerkins ""528xe2x80x9d), which is hereby incorporated by reference as if recited in full herein. This approach combined classical genetic mutant selection and fermentation improvement with genetic engineering of the riboflavin biosynthetic genes by deregulating and increasing the level of gene expression. In this system, the expression of the rib genes was increased by mutating the flavokinase encoding ribC gene, by linking the rib genes to strong, constitutive promoters, and by increasing the copy number of the rib genes.
For example, in the engineered rib operon present in plasmid pRF69 disclosed by Perkins ""528, the entire ribP1 promoter and most of the regulatory leader region were deleted and replaced with a constitutive phage SPO1promoter, P15. See, FIG. 1B. In addition, the phage promoter was introduced between the ribB and ribA genes to further increase the transcription of the corresponding downstream genes. Finally, pRF69 was provided with a chloramphenicol resistance gene downstream of the rib genes. pRF69 was targeted by single cross-over transformation into the rib operon of the host microorganism RB50, which contained mutations deregulating purine biosynthesis and which contained a mutation in the ribC gene deregulating riboflavin biosynthesis.
The genomic structure resulting from single crossover transformation of RB50 with pRF69 includes a chloramphenicol resistance gene flanked by the wild type rib operon at one end and by the engineered rib operon of pRF69 at the other end. The iterative elements within this structure originate increased copy numbers of the resistance gene and of the flanking rib operon upon selection of the pRF69 transformed bacteria for increased chloramphenicol resistance.
Enhanced transcription of the rib genes in RB50 containing multiple (n) copies of the modified rib operon of pRF69 (i.e., RB50::[pRF69]n) has been confirmed by Northern blot analysis. Unlike wild-type B. subtilis, which accumulated very small amounts of RNA transcript that covered the entire rib operon, RB50::[pRF69]n accumulated large amounts of shorter transcripts that covered primarily the first two genes of the operon. The second P15 promoter engineered upstream of ribA gave rise to significant accumulation of RNA transcripts that covered the three downstream genes of the rib operon. See, Perkins, J. B., et al., J. Ind. Microbiol Biotechnol., 22:8-18 (1999).
In a riboflavin fed batch fermentation reactor containing, for example, B. subtilis RB50::[pRF69]n, biomass and riboflavin are produced from a common fermentation substrate, glucose. The rate by which glucose is pumped into the reactor (xe2x80x9cglucose feeding ratexe2x80x9d) is critical to its utilization in the production of biomass and riboflavin, respectively. A fast glucose feeding rate allows the culture to grow at elevated rates causing an excess of biomass formation and a reduction of the riboflavin yield. Glucose feeding rates that are too slow, however, while lowering biomass production, result in low riboflavin productivity. Because low yield, low productivity, or both increase riboflavin production costs, a balance must be struck between biomass and riboflavin production by carefully regulating the glucose feeding rate in commercial riboflavin fermentation reactors.
In view of the deficiencies noted above, it would be desirable to optimize production of a target fermentation product, such as riboflavin, while concurrently maintaining biomass production at a level that is most efficient for the size and type of reactor used.
One embodiment of the present invention is a process for producing a target fermentation product. This process includes providing a fermentation medium containing a recombinantly-produced microorganism that over-produces a target fermentation product and that contains a mutation which causes auxotrophic growth of the microorganism, wherein the auxotrophy within the microorganism does not compromise the ability of the microorganism to produce the target fermentation product. The medium is then supplied with all substrates required for production of the fermentation product, a substrate for the target fermentation product, and a substrate complementing the auxotrophy. The former substrate(s) is/are provided in excess, ensuring maximal productivity. The latter substrate (i.e., substrate complementing the auxotrophy) is supplied in limited amounts to maintain biomass formation at a low rate.
Another embodiment of the present invention is a process for decoupling production of a target fermentation product from biomass production in a fermentation medium. This process includes providing a recombinantly produced microorganism that has been engineered to contain a polynucleotide sequence which encodes the biosynthetic enzymes for a target fermentation product. In this process, the maximal production of the target fermentation product is dependent on an unlimited supply of a target fermentation product substrate for the microorganism. Next, an auxotrophy is introduced into the microorganism to control biomass production by limiting the concentration of a substrate complementing the auxotrophy in the fermentation medium. A fermentation production microorganism made by the process set forth above is also provided.
The present invention also includes as a further embodiment a polynucleotide, which is selected from SEQ ID NO:1, an auxotrophy-introducing homolog or fragment of SEQ ID NO:1, or a polynucleotide sequence containing an insertion, deletion, or substitution of SEQ ID NO:1, which polynucleotide retains the ability to cause an auxotrophy in a host cell.
Another embodiment of the present invention is a host cell transformed with a polynucleotide sequence including SEQ ID NO:1, a homolog or a fragment of SEQ ID NO:1 which retains its ability to cause an auxotrophy in the host cell, or a polynucleotide sequence containing an insertion, deletion, or substitution of SEQ ID NO:1, which polynucleotide retains the ability to cause an auxotrophy in the host cell.
The present invention also provides as another embodiment a riboflavin production microorganism RB50 containing multiple copies of the engineered rib operon pRF69 and transformed with the polynucleotide sequence SEQ ID NO:1.